yannrichet / rsession Goto Github PK

What steps will reproduce the problem?
1. On MacOSX, with R 2.15.2 and JDK6
2. Rsession session = Rsession.newInstanceTry(System.out, null);
    session.loadPackage("robust");

What is the expected output? What do you see instead?
Evaluation of expressions work, but load libraries fail
run:
! No Rserve conf given. Trying to use R://localhost
[eval] library(robust)
!! [exception] eval failed
java.net.SocketException: Broken pipe
  library(robust)
  request package robust loading...
    at java.net.SocketOutputStream.socketWrite0(Native Method)
!! [exception] eval failed
  loadedpacks<-.packages()
!! [exception] eval failed
  is.element(set=loadedpacks,el='robust')
  package robust is not loaded.
!! [exception] eval failed
  rm(loadedpacks)
!   package robust loading failed.
[eval] rnorm(1000)
!! [exception] eval failed
  rnorm(1000)
    at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:92)
    at java.net.SocketOutputStream.write(SocketOutputStream.java:124)
    at org.rosuda.REngine.Rserve.protocol.RTalk.request(RTalk.java:205)
    at org.rosuda.REngine.Rserve.protocol.RTalk.request(RTalk.java:180)
    at org.rosuda.REngine.Rserve.protocol.RTalk.request(RTalk.java:250)
    at org.rosuda.REngine.Rserve.RConnection.eval(RConnection.java:230)
    at org.rosuda.REngine.Rserve.RConnection.parseAndEval(RConnection.java:451)
    at org.rosuda.REngine.REngine.parseAndEval(REngine.java:108)
    at org.math.R.Rsession.silentlyEval(Rsession.java:965)
    at org.math.R.Rsession.silentlyEval(Rsession.java:941)
    at org.math.R.Rsession.isPackageLoaded(Rsession.java:601)
    at org.math.R.Rsession.loadPackage(Rsession.java:839)
    at rsessiontest.RSessionTest.main(RSessionTest.java:63)
java.net.SocketException: Broken pipe
    at java.net.SocketOutputStream.socketWrite0(Native Method)
    at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:92)
    at java.net.SocketOutputStream.write(SocketOutputStream.java:124)
    at org.rosuda.REngine.Rserve.protocol.RTalk.request(RTalk.java:205)
    at org.rosuda.REngine.Rserve.protocol.RTalk.request(RTalk.java:180)
    at org.rosuda.REngine.Rserve.protocol.RTalk.request(RTalk.java:250)
    at org.rosuda.REngine.Rserve.RConnection.eval(RConnection.java:230)
    at org.rosuda.REngine.Rserve.RConnection.parseAndEval(RConnection.java:451)
    at org.rosuda.REngine.REngine.parseAndEval(REngine.java:108)
    at org.math.R.Rsession.silentlyEval(Rsession.java:965)
    at org.math.R.Rsession.silentlyEval(Rsession.java:941)
    at org.math.R.Rsession.isPackageLoaded(Rsession.java:614)
    at org.math.R.Rsession.loadPackage(Rsession.java:839)
    at rsessiontest.RSessionTest.main(RSessionTest.java:63)
java.net.SocketException: Broken pipe
    at java.net.SocketOutputStream.socketWrite0(Native Method)
    at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:92)
    at java.net.SocketOutputStream.write(SocketOutputStream.java:124)
    at org.rosuda.REngine.Rserve.protocol.RTalk.request(RTalk.java:205)
    at org.rosuda.REngine.Rserve.protocol.RTalk.request(RTalk.java:180)
    at org.rosuda.REngine.Rserve.protocol.RTalk.request(RTalk.java:250)
    at org.rosuda.REngine.Rserve.RConnection.eval(RConnection.java:230)
    at org.rosuda.REngine.Rserve.RConnection.parseAndEval(RConnection.java:451)
    at org.rosuda.REngine.REngine.parseAndEval(REngine.java:108)
    at org.math.R.Rsession.silentlyEval(Rsession.java:965)
    at org.math.R.Rsession.eval(Rsession.java:997)
    at org.math.R.Rsession.eval(Rsession.java:1016)
    at rsessiontest.RSessionTest.main(RSessionTest.java:65)
BUILD SUCCESSFUL (total time: 2 seconds)

What version of the product are you using? On what operating system?
Mac OSX 10.7, JDK 6, R 2.15.2

Please provide any additional information below.
Interestingly, I have a Macbook Pro and iMac, with the same configs. The same 
programs works on the Macbook Pro but fails on iMac. Still haven't figured out 
what caused the issue.

For me it is often helpful to show an R-plot within a JPanel. Here's what
the core piece of code which is necessary to do so:

        String device = "jpeg"; // device we'll call (this would work with
pretty much any bitmap device)

        String tempFileName = "rmPlotFile." + device;
        REXP xp = connection.parseAndEval("try(" + device + "('" +
tempFileName + "',quality=95, width = " + width + ", height = " + height +
"))");

        if (xp.inherits("try-error")) { // if the result is of the class
try-error then there was a problem
            System.err.println("Can't open " + device + " graphics
device:\n" + xp.asString());
            // this is analogous to 'warnings', but for us it's sufficient
to get just the 1st warning
            REXP w = connection.eval("if (exists('last.warning') &&
length(last.warning)>0) names(last.warning)[1] else 0");
            if (w.isString()) System.err.println(w.asString());
            return null;
        }

        // ok, so the device should be fine - let's plot - replace this by
any plotting code you desire ...
        String preparedScript = RUtils.prepare4RExecution(script);

        String[] splitScript = preparedScript.split(";");
        for (String s : splitScript) {
            try {
                connection.parseAndEval(RUtils.prepare4RExecution(s + ";"));
            } catch (REngineException e) {
                throw new RuntimeException("Error while executing line: " +
s, e);
            }
        }
//        connection.parseAndEval(preparedScript);

        // close the image
        connection.parseAndEval("dev.off();");

        // There is no I/O API in REngine because it's actually more
efficient to use R for this
        // we limit the file size to 1MB which should be sufficient and we
delete the file as well
        xp = connection.parseAndEval("r=readBin('" + tempFileName +
"','raw',2024*2024); unlink('" + tempFileName + "'); r");

        // now this is pretty boring AWT stuff - create an image from the
data and display it ...
        return Toolkit.getDefaultToolkit().createImage(xp.asBytes());

Maybe it would be nice to have this available directly in Rsession. If not 
just close the issue...

	// Added by Jean 2023/05/23
	public Properties properties = null;

	// Added by Jean 2023/05/23
	public RserverConf(String RserverHostName, int RserverPort, String login, String password, Properties props) {

		this.host = RserverHostName;
		this.port = RserverPort;
		this.login = login;
		this.password = password;
		this.properties = props;
	}

	public synchronized RConnection connect() {
		// Logger.err.print("Connecting " + toString()+" ... ");

		TimeOut t = new TimeOut() {

			protected Object defaultResult() {
				return -2;
			}

			protected Object command() {
				// Added by Jean 2023/05/23
				String tls = "false";
				if (properties != null) {
					try {
						tls = properties.getProperty("tls");
						if (tls == null || tls != "true")
							tls = "false";
					} catch (Exception ex) {
					}
				}

				int n = 10;
				while ((n--) > 0) {

					// Modified by Jean 2023/05/23
					if (tls == "false") {

						try {
							if (host == null) {
								if (port > 0) {
									connection = new RConnection(DEFAULT_RSERVE_HOST, port);
								} else {
									connection = new RConnection(DEFAULT_RSERVE_HOST, DEFAULT_RSERVE_PORT);
								}
								if (connection.needLogin()) {
									connection.login(login, password);
								}
							} else {
								if (port > 0) {
									connection = new RConnection(host, port);
								} else {
									connection = new RConnection(host);
								}
								if (connection.needLogin()) {
									connection.login(login, password);
								}
							}
							return 0;
						} catch (RserveException ex) {
							Log.Err.println("Failed to connect on host:" + host + " port:" + port + " login:" + login
									+ "\n  " + ex.getMessage());
						}
						// Added by Jean for tls connection 2023/05/23
					} else {
						SSLSocketFactory sslsocketfactory = (SSLSocketFactory) SSLSocketFactory.getDefault();
						SSLSocket sslsocket;
						try {
							if (host == null) {
								host = DEFAULT_RSERVE_HOST;
							}
							if (port > 0) {
							} else {
								port = 6311;
							}
							// connection = new RConnection();
							sslsocket = (SSLSocket) sslsocketfactory.createSocket(host, port);
							// Connect to the remote server.
							connection = new RConnection(sslsocket);

							if (connection.needLogin()) {
								connection.login(login, password);
							}
							return 0;
						} catch (Exception ex) {
							Log.Err.println("Failed to connect: " + ex.getMessage());
						}

					}
				}
				return -1;
			}
		};

		try {
			t.execute(CONNECT_TIMEOUT);
		} catch (Exception e) {
			Log.Err.println("Connection " + toString() + " failed: " + e.getMessage());
		}

		if (((Integer) t.getResult()) != 0) {
			Log.Err.println("Connection " + toString() + " failed.");
			return null;
		} else {
			return connection;
		}
	}

root@VM-0-14-ubuntu:/home/ubuntu# vi /etc/Rserv.conf

// Enable remote login
remote enable
// Authentication required
auth required
// Disable plaintext
plaintext disable
// Use utf-8
encoding utf8
//Enable remote control or R process
control enable
//Use qap+tls protocol
qap.tls.port 6311
//Rserve server key
tls.key /root/cert/server.key
//Selfsigned Rserve server cert
tls.cert /root/cert/server.crt
//Selfsigned CA cert
tls.ca /root/cert/demoCA/cacert.pem
//Disable unencypted qap
qap disable

	public static Rsession initRserve() throws IOException {
		Properties prop = new Properties();
		prop.setProperty("tls", "true");
		RserverConf rconf = new RserverConf(host, 6311, "user", "password", prop);
		rsession = (RserveSession)new RserveSession(System.out, null, rconf);
		return rsession;
	}

What steps will reproduce the problem?

public static void main(String[] args) throws REXPMismatchException, 
RserveException {


        Rsession s = Rsession.newInstanceTry(System.out, null);
    //    RConnection s = new RConnection();

       String string;

       string = "x = 2 + 4" + "\n"
               + "x" + "\n"
               + "x + 2";

       String y;

       y = s.eval(string).asString();

       System.out.println(y);

        s.end();


}

What is the expected output? What do you see instead?


What version of the product are you using? On what operating system?
Any operating system

Please provide any additional information below.

If you use Rconnection instead, it works just fine

public void testTsession(){
    RserverConf rconf = new RserverConf("127.0.0.1", 6311, "", "", new Properties());
    Rsession s = null;
    s = Rsession.newInstanceTry(System.out, rconf);
    s.eval("warning2error <- function(code=\"\") { tryCatch(code, warning = function(e) stop(e)) }");
    s.eval("warning2error(warning(\'hahaha\'))", true);
    s.end();
}

@Test
public void testAll(){
    for(int i=0; i<25; i++) {
        testTsession();
    }
}

    /**
     * Get file from R environment to user OutputStream
     *
     * @param os local OutputStream file
     * @param remoteFile R environment file name
     */
    public synchronized void getFile(OutputStream os, String remoteFile) {
        try {
            if (((REXP) silentlyRawEval("file.exists('" + remoteFile.replace("\\", "/") + "')", TRY_MODE)).asInteger() != 1) {
                log(HEAD_ERROR + IO_HEAD + "file " + remoteFile + " not found.", Level.ERROR);
            }
        } catch (Exception ex) {
             log(HEAD_ERROR + ex.getMessage() + "\n  getFile(File remoteFile=" + remoteFile + ")", Level.ERROR);
            return;
        }

        InputStream is = null;
        //synchronized (R) {
        try {
            is = R.openFile(remoteFile.replace("\\", "/"));
            //os = new BufferedOutputStream(new FileOutputStream(localfile));
            IOUtils.copy(is, os);
            log(IO_HEAD + "File " + remoteFile + " received.", Level.INFO);
            is.close();
        } catch (IOException e) {
            log(HEAD_ERROR + IO_HEAD + R.getLastError() + ": file " + remoteFile + " not transmitted.\n" + e.getMessage(), Level.ERROR);
        } finally {
            IOUtils.closeQuietly(is);
         }
        //}
    }

        assert engine.eval("paste(sep='<br/>',\n"
                + "        paste('<HTML name=\"minimum\">minimum is ',0.1),\n"
                + "        paste(sep='',\n"
                + "            'found at ',\n"
                + "            paste(collapse='; ',paste(c('x1','x2'),'=',c(.5,.6))),\n"
                + "            '<br/><img src=\"',\n"
                + "            'files',\n"
                + "            '\" width=\"',600,'\" height=\"',600,\n"
                + "            '\"/></HTML>'))").toString().contains("\"minimum\"");

        assert engine.eval("paste0(\"<HTML name='minimum'>minimum is \",0.1,\n"
                + "                \" found at \",\n"
                + "                paste0(paste(c('x1','x2'),'=',c(.5,.6), collapse=';')),\n"
                + "                \"<br/><img src='\",\n"
                + "                \"files\",\n"
                + "                \"' width='600' height='600'/></HTML>\")").toString().contains("'minimum'");

@Test
    public void testHardConcurrency() throws REXPMismatchException, InterruptedException {

I think some casts are needed in order to get the example java code to compile 
and run, see below.

import java.io.File;

import static org.math.R.Rsession.*;
import org.math.R.Rsession;
import org.rosuda.REngine.REXPMismatchException;

public class RsessionHelper {
    public static void main(String args[]) throws REXPMismatchException {
        Rsession s = Rsession.newInstanceTry(System.out, null);

        double[] rand = (double[]) (cast(s.eval("rnorm(10)"))); // create java variable from R command

        s.set("c", Math.random()); // create R variable from java one

        s.save(new File("save.Rdata"), "c"); // save variables in save.Rdata
        s.rm("c"); // delete variable in R environment
        s.load(new File("save.Rdata")); // load R variable from save.Rdata

        s.set("df", new double[][] { { 1, 2, 3 }, { 4, 5, 6 }, { 7, 8, 9 }, { 10, 11, 12 } }, "x1", "x2", "x3"); // create data frame from
                                                                                                                 // given vectors
        double value = (Double) (cast(s.eval("df$x1[3]"))); // access one value in data frame

        s.toJPEG(new File("plot.jpg"), 400, 400, "plot(rnorm(10))"); // create jpeg file from R graphical command (like plot)

        String html = s.asHTML("summary(rnorm(100))"); // format in html using R2HTML
        System.out.println(html);

        String txt = s.asString("summary(rnorm(100))"); // format in text
        System.out.println(txt);

        System.out.println(s.installPackage("sensitivity", true)); // install and load R package
        System.out.println(s.installPackage("wavelets", true));

        s.end();
    }
}

package test.jean;

import java.util.Properties;

import org.math.R.RserveSession;
import org.math.R.RserverConf;

public class RserveTest {

	public static void main(String args[]) {
		try {
			Properties prop = new Properties();
			prop.setProperty("tls", "true");
			RserverConf rconf = new RserverConf(host_ip, 6311, "user", "password", prop);
			RserveSession r = (RserveSession)new RserveSession(System.out, null, rconf);
			// create java variable from R command
			double[] rand = (double[]) r.eval("rnorm(10)"); 
			// Try to load source R script into remote R process
			r.eval("source(\"/home/jean/R/testChinese.R\")",false);
                        r.eval("testChinese()");
			System.out.println(r.asString(r.eval("rc$st")));
						
			r.end();
		} catch (Exception e) {
			e.printStackTrace();

		}
	}
}

testChinese<-function(){
  test<-c("Rserve中文测试。")
  rc<<-list(st=test)
  return(rc)  
}

Will start Rserve session using: R://rserve:rserve@[email protected]:6311


[eval] [?] rnorm(10)


[1.1353798479890087, 0.7775232440858648, 1.6027476936447704, 0.9962751826116198, -0.051552560170046106, -1.0327774491148507, 1.267379942526929, -0.7154783097683929, 0.2075579485456512, 1.2805371369512242]
[eval] source("/home/jean/R/testChinese.R")


java.lang.NullPointerException
	at org.math.R.RserveSession.toString(RserveSession.java:1208)
	at org.math.R.RserveSession.toString(RserveSession.java:1187)
	at org.math.R.Rsession.rawEval(Rsession.java:945)
	at org.math.R.Rsession.eval(Rsession.java:1006)
	at test.jean.RserveTest.main(RserveTest.java:19)

math.squeeze(math.subset(__this__.Sys__info(), R._index('release')))

package test.jean;

import java.util.Properties;

import org.math.R.RserveSession;
import org.math.R.RserverConf;

public class RserveTest {

	public static void main(String args[]) {
		try {
			Properties prop = new Properties();
			prop.setProperty("tls", "true");
			RserverConf rconf = new RserverConf(host, 6311, "user", "password", prop);
			RserveSession r = (RserveSession)new RserveSession(System.out, null, rconf);
			// create java variable from R command
			double[] rand = (double[]) r.eval("rnorm(10)"); 
			// Use r.eval() to source script will cause java.lang.NullPointerException
			//r.eval("source(\"/home/jean/R/testChinese.R\")",false);
			// So r.voidEval() to load.
			r.voidEval("source(\"/home/jean/R/testChinese.R\")");
			r.eval("testChinese()");
			System.out.println(r.asString(r.eval("rc$st")));
					
			r.end();
		} catch (Exception e) {
			e.printStackTrace();

		}
	}
}

source("/home/jean/R/testChinese.R")
R! Error in file(con,"w"):无法打开链结
此外: Warning message:
In file(con,"w"):
无法打开文件'/tmp/RtmpGLcOIq/file7ccc5c5ae965.sh': 没有那个文件或目录
at org.math.R.Rsession.voidEval(Rsession.java:864
at org.math.R.Rsession.voidEval(Rsession,java:885)
at MelbourneRserve.calRServe(MelbourneRserve.java:70)
at MelbourneRserve .doGet(MelbourneRserve.java:39)
at javax.servlet.http.HttpServlet.service(HttpServlet.iava:670)
<22 internal lines>

testChinese<-function(){
  test<-c("Rserve中文测试。")
  rc<<-list(st=test)
  return(rc)  
}

What steps will reproduce the problem?
1. Start Rserve within R with: Rserve()
2. create an Rsession instance in java with:
Rsession.newLocalInstance(System.out, null)
3. The error msg which show is up is:
Connecting R://localhost:6314
Rserve R://localhost:6314 is not accessible.

If I specify the Rserve port in R via: Rserve(port=6315), the error msg
remains and the port is simply incremented compared to the Rserve-port.
This indicates that there is some kind of communication between Rsession
and Rserve.